Research workbench
Crystal structure of fxa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 2
Analyse Crystal structure of fxa in complex with 4,4-disubstituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W3I
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X, heavy chain; Coagulation factor X, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- L1C, CA
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X, heavy chain (EC 3.4.21.6) | protein | 234 | 14% helix, 35% strand | P00742 |
| B | Coagulation factor X, light chain (EC 3.4.21.6) | protein | 50 | 8% helix, 32% strand | P00742 |
Ligands and binding sites
- L1C · (2R,4S)-N^1^-(4-chlorophenyl)-4-(2,4-difluorophenyl)-4-hydroxy-N^2^-(2-oxo-2H-1,3'-bipyridin-6'-yl)pyrrolidine-1,2-dicarboxamide · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.46 | 0.78 | 31 | L1C |
| 2 | 154 | 0.45 | 0.75 | 29 | empty |
| 3 | 54 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2W3I · Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide… · the same entry in another collection · chain A against A, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00742
- Elsewhere: RCSB PDB 2W3I · PDBe 2W3I · UniProt P00742
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